Contacts of the helix formed by residues 482 - 504 (chain B) in PDB entry 3BYH
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 482 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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473B VAL* 5.0 5.3 - - - +
477B ASP* 2.9 39.1 + - + +
480B GLN* 3.4 3.5 + - + +
481B GLY* 1.3 71.0 - - - +
483B LYS* 1.3 58.2 + - - +
484B LYS* 3.1 13.4 + - - +
485B LEU* 2.9 38.8 + - + +
486B ILE* 2.9 30.6 + - - +
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Residues in contact with LYS 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391B THR* 4.6 9.8 - - + +
415B PHE* 3.7 55.3 - - + -
481B GLY 2.6 17.2 + - - +
482B ASN* 1.3 69.6 + - - +
484B LYS* 1.3 60.4 + - - +
486B ILE* 4.3 0.9 - - - -
487B LEU* 2.9 39.7 + - + +
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Residues in contact with LYS 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ASP* 4.5 17.6 + - - +
482B ASN* 3.1 9.3 + - - +
483B LYS* 1.3 79.2 - - - +
485B LEU* 1.3 61.2 + - - +
487B LEU* 4.2 6.3 - - - +
488B GLY* 3.2 18.4 + - - -
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Residues in contact with LEU 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B ILE* 4.7 7.2 - - + -
470B LEU* 3.6 29.8 - - + -
473B VAL* 4.0 27.1 - - + -
474B ALA 4.3 2.2 - - - +
477B ASP* 3.3 34.5 - - + -
478B ILE* 4.0 22.0 - - + +
482B ASN* 2.9 22.2 + - + +
484B LYS* 1.3 75.0 - - - +
486B ILE* 1.3 61.3 + - + +
488B GLY* 3.2 1.2 + - - -
489B LEU* 2.8 32.7 + - + +
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Residues in contact with ILE 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B VAL 4.6 2.7 - - - +
415B PHE* 4.2 25.1 - - + +
418B VAL* 3.3 38.1 - - + -
424B LEU* 5.7 2.9 - - + -
478B ILE* 4.2 22.0 - - + +
481B GLY* 4.1 23.1 - - - +
482B ASN 2.9 22.0 + - - +
483B LYS* 3.9 5.6 - - - +
485B LEU* 1.3 78.1 - - + +
487B LEU* 1.3 57.0 + - - +
489B LEU* 3.9 6.6 - - - +
490B LEU* 3.0 52.7 + - + +
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Residues in contact with LEU 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391B THR* 4.4 14.6 - - + +
394B ASP* 3.8 38.8 - - + +
395B GLU* 4.7 1.1 - - - +
398B TYR* 4.2 16.7 - - + -
414B VAL* 5.4 1.1 - - + -
415B PHE* 3.5 34.1 - - + -
483B LYS* 2.9 28.0 + - + +
484B LYS* 4.2 5.8 - - - +
486B ILE* 1.3 73.7 - - - +
488B GLY* 1.3 61.3 + - - +
490B LEU* 3.4 8.5 + - + +
491B TRP* 2.9 30.0 + - - +
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Residues in contact with GLY 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ASN 5.0 2.6 - - - +
93A GLU* 6.1 0.7 - - - -
95A ARG* 4.1 0.3 - - - -
470B LEU* 5.7 1.3 - - - -
484B LYS 3.2 14.1 + - - -
485B LEU* 3.6 3.4 - - - -
487B LEU* 1.3 81.2 - - - +
489B LEU* 1.3 60.6 + - - +
491B TRP* 3.6 6.1 + - - +
492B GLN* 3.3 33.7 + - - +
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Residues in contact with LEU 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B LEU* 3.8 21.8 - - + -
428B LEU* 5.9 2.0 - - + -
459B VAL* 3.7 32.5 - - + +
460B ILE* 5.0 6.7 - - + -
463B GLY* 5.0 8.5 - - - -
468B PHE* 4.2 20.9 - - + -
470B LEU* 4.7 14.8 - - + +
478B ILE* 4.3 9.6 - - + -
485B LEU* 2.8 29.0 + - + +
486B ILE* 3.9 7.0 - - - +
488B GLY* 1.3 73.8 - - - +
490B LEU* 1.3 62.4 + - - +
492B GLN* 3.6 6.2 + - - +
493B LEU* 3.0 40.2 + - + +
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Residues in contact with LEU 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B TYR* 3.8 38.3 - - + -
401B TRP* 4.3 9.2 - - + -
402B ILE* 3.9 26.2 - - + -
414B VAL* 4.6 15.0 - - + -
418B VAL* 5.8 2.2 - - + -
424B LEU* 4.1 23.1 - - + -
427B VAL* 5.7 0.9 - - + -
486B ILE* 3.0 42.7 + - + +
487B LEU* 3.7 5.8 - - + +
488B GLY 3.3 0.2 - - - -
489B LEU* 1.3 74.3 - - + +
491B TRP* 1.3 65.8 + - - +
493B LEU* 3.1 12.6 + - + +
494B MET* 2.8 23.6 + - - +
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Residues in contact with TRP 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A PHE* 6.0 2.2 - + - -
28A ARG* 5.0 13.9 - - - +
93A GLU 4.6 6.0 + - - -
94A LEU 3.6 13.1 + - - -
95A ARG* 3.2 35.6 - - + +
398B TYR* 3.2 30.2 - - - +
487B LEU 2.9 15.6 + - - +
488B GLY* 3.8 7.2 - - - +
489B LEU 3.4 0.2 - - - -
490B LEU* 1.3 75.6 - - - +
492B GLN* 1.3 55.7 + - - +
494B MET* 2.9 11.6 + - - +
495B ARG* 2.8 36.8 + - + +
605B ASN* 5.6 1.6 - - - -
606B GLN* 5.9 0.4 - - + -
607B LYS* 0.9 133.5 - - + -
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Residues in contact with GLN 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A TYR 2.5 28.1 + - - -
92A ASN* 2.9 16.3 - - - +
95A ARG* 0.8 279.9 + - + +
468B PHE* 4.0 3.8 - - + +
469B SER 2.9 14.1 + - - +
470B LEU* 4.6 2.9 - - - +
488B GLY 3.3 19.6 + - - +
489B LEU* 3.9 6.2 - - - +
491B TRP* 1.3 79.4 - - - +
493B LEU* 1.3 55.9 + - - +
495B ARG* 3.9 2.0 - - - +
496B PHE* 2.9 24.4 + - - +
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Residues in contact with LEU 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ARG* 4.1 0.2 - - - +
401B TRP* 3.8 12.6 - - + -
424B LEU* 4.2 10.5 - - + -
427B VAL* 4.1 22.2 - - + -
428B LEU* 3.5 35.2 - - + -
431B VAL* 4.1 11.4 - - + +
459B VAL* 6.4 0.2 - - + -
466B LEU* 5.2 1.1 - - + -
468B PHE* 3.7 18.6 - - + -
489B LEU* 3.0 37.1 + - + +
490B LEU* 3.1 24.7 + - + +
492B GLN* 1.3 75.3 - - - +
494B MET* 1.3 58.5 + - - +
496B PHE* 3.6 2.0 - - + +
497B HIS* 3.0 30.8 + - - +
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Residues in contact with MET 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397B CYS* 4.0 9.6 - - - -
398B TYR* 3.8 24.9 - - + -
401B TRP* 3.5 46.5 - - + +
490B LEU 2.8 11.9 + - - +
491B TRP* 3.3 10.8 - - + +
493B LEU* 1.3 78.1 - - - +
495B ARG* 1.3 61.3 + - - +
497B HIS* 3.8 2.1 - - - +
498B MET* 3.1 23.6 + - + +
605B ASN* 5.3 1.6 - - - +
607B LYS* 3.8 26.9 - - + +
608B MET* 2.2 49.8 - - + -
611B ILE* 5.2 3.8 - - + +
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Residues in contact with ARG 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ASP* 5.1 10.3 + - - -
21A PHE* 5.9 1.2 - - - -
94A LEU 4.3 2.6 + - - -
95A ARG* 1.6 51.0 + - - +
96A VAL* 2.8 34.8 - - - +
97A ALA* 3.5 7.5 - - - +
100A GLU* 5.8 0.8 + - - -
101A HIS* 5.2 3.2 + - - -
468B PHE* 6.2 0.8 - - - -
491B TRP* 2.8 30.3 + - + +
492B GLN* 4.0 4.3 - - - +
494B MET* 1.3 71.9 - - - +
496B PHE* 1.3 67.9 + - - +
498B MET* 3.4 6.7 + - - +
499B LEU* 3.1 51.8 + - + +
607B LYS* 3.4 23.1 - - - +
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Residues in contact with PHE 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ARG* 4.1 0.2 - - - +
431B VAL* 3.3 35.0 - - + -
432B SER* 4.3 12.6 - - - -
466B LEU* 3.8 36.3 - - + -
468B PHE* 3.6 25.6 - + + -
492B GLN 2.9 21.4 + - - +
493B LEU* 3.6 4.7 - - + +
495B ARG* 1.3 80.1 - - - +
497B HIS* 1.3 62.3 + - - +
499B LEU* 3.4 7.8 + - + +
500B GLN* 3.0 60.3 + - + +
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Residues in contact with HIS 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401B TRP* 4.2 11.3 + - + +
405B LEU* 4.0 29.4 - - + +
430B LYS* 4.8 5.6 + - + -
431B VAL* 3.4 43.5 - - + +
493B LEU 3.0 14.1 + - - +
494B MET 3.8 4.7 - - - +
495B ARG 3.3 0.2 - - - -
496B PHE* 1.3 76.9 - - - +
498B MET* 1.3 57.3 + - - +
500B GLN* 3.3 5.8 + - + +
501B LEU* 3.0 63.6 + - + +
611B ILE* 5.0 5.0 - - + +
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Residues in contact with MET 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494B MET* 3.1 17.3 + - + +
495B ARG* 3.6 7.6 - - + +
496B PHE 3.3 0.2 - - - -
497B HIS* 1.3 76.7 - - - +
499B LEU* 1.3 64.0 + - + +
501B LEU* 3.3 10.6 + - + -
502B LEU 3.1 18.4 + - - -
516B ASP* 3.5 3.8 - - - +
519B ILE* 4.0 9.2 - - + -
607B LYS* 3.9 9.0 - - + +
610B LEU* 1.8 82.3 - - + +
611B ILE* 2.7 45.2 - - + +
614B ALA* 4.2 1.8 - - + -
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Residues in contact with LEU 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ASP* 4.0 10.8 - - - +
100A GLU* 5.7 5.2 - - - +
495B ARG* 3.1 57.8 + - + +
496B PHE* 3.9 6.5 - - + +
498B MET* 1.3 76.0 - - + +
500B GLN* 1.3 62.0 + - - +
502B LEU* 3.4 2.6 + - - +
503B LYS* 2.9 30.3 + - - +
515B THR* 5.1 0.2 - - - -
516B ASP* 3.2 30.5 - - - +
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Residues in contact with GLN 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431B VAL 4.7 6.6 - - - +
496B PHE* 3.0 58.0 + - + +
497B HIS* 3.6 9.4 - - + +
498B MET 3.3 0.2 - - - -
499B LEU* 1.3 79.7 - - - +
501B LEU* 1.3 63.2 + - - +
503B LYS* 3.3 29.3 + - - +
504B SER* 3.0 22.5 + - - -
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Residues in contact with LEU 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497B HIS* 3.0 43.9 + - + +
498B MET* 3.5 13.5 - - + +
500B GLN* 1.3 76.5 - - - +
502B LEU* 1.3 60.2 + - - +
504B SER* 2.5 28.2 + - - +
505B LEU* 3.2 7.1 - - - +
514B MET* 3.0 3.8 - - - +
519B ILE* 4.9 3.8 - - + -
611B ILE* 3.6 34.8 - - + -
614B ALA* 5.0 8.7 - - + -
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Residues in contact with LEU 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498B MET 3.1 7.2 + - - +
499B LEU 3.7 4.3 - - - +
501B LEU* 1.3 73.6 - - - +
503B LYS 1.3 48.9 - - - +
514B MET* 1.4 59.7 - - - +
515B THR* 1.8 49.7 + - - +
516B ASP* 1.1 104.1 - - + +
519B ILE* 2.2 48.0 - - + -
610B LEU* 3.8 5.6 - - + -
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Residues in contact with LYS 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B LEU 2.9 17.3 + - - +
500B GLN* 3.4 29.9 + - - +
502B LEU* 1.3 67.3 - - - +
504B SER* 1.3 47.2 + - - +
506B ARG* 3.6 34.8 - - - +
513B GLU* 1.9 24.0 + - - +
514B MET 1.3 49.3 + - - +
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Residues in contact with SER 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B GLN 3.0 11.5 + - - -
501B LEU* 2.5 27.1 + - - +
503B LYS* 1.3 69.6 - - - +
505B LEU* 1.3 59.6 + - - +
506B ARG 3.3 2.7 + - - +
513B GLU 3.8 6.6 + - - +
514B MET* 1.8 17.0 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il